I had a similar problem. 1mm in the y and 2mm in the x. Problem was circles were round but only 1mm shorter than specified.

used mach 3s auto setup. The one where it asks you to go a certain distance and then you measure it. Seems to have worked.

Initially i thought it was backlash but when I changed this it made it worse.

Im using a 8mm threaded rod on all axis and worked out it should be 320 steps per mm. With the mach setup it said I needed 326.xxx on one axis and something similar on the other.

Maybe the threaded rod wasnt exactly 1.25mm.

Anyway problem sorted.